We report extraordinary variation in the number and the chromosomal location of ribosomal DNA (rDNA) arrays within populations of the alpine grasshopper Podisma pedestris; even greater differences were found between populations. The sites were detected by in situ hybridisation of labelled rDNA to chromosomal preparations. The total number of rDNA sites in an individual varied from three to thirteen. In the most extreme case, individuals from populations only 10 km apart had no rDNA loci in common. A survey of the geographical distribution of this variation identified clusters of populations with relatively similar chromosomal distribution of rDNA loci. These clusters correspond to those identified earlier by analysis of rDNA sequences. To explain this geographical clustering, we reconstructed the post-glacial colonisation of the region by assuming that the species' distribution has ascended to its current altitudinal range as the climate warmed. The reconstruction suggests that each cluster is descended from a colonisation route up a different alpine valley. That history would imply rapid establishment of rDNA differences, conceivably during the last 10,000 years since the last glaciation. The proposal for rapid change is consistent with the extensive within-population variation, which indicates that the processes responsible for the change in rDNA's chromosomal location continue to occur at a higher rate. We discuss whether our reconstruction of colonisation routes implies movement of the hybrid zone, which would indicate that a neo-XY sex chromosome system has spread through extant populations.